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Alanine racemase (EC 5.1.1.1)

 ALR_GEOSE               Reviewed;         388 AA.
P10724;
01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
01-NOV-1997, sequence version 2.
15-MAR-2017, entry version 128.
RecName: Full=Alanine racemase {ECO:0000255|HAMAP-Rule:MF_01201};
EC=5.1.1.1 {ECO:0000255|HAMAP-Rule:MF_01201, ECO:0000269|PubMed:10079072, ECO:0000269|PubMed:12203980, ECO:0000269|PubMed:12741835};
Name=alr; Synonyms=dal;
Geobacillus stearothermophilus (Bacillus stearothermophilus).
Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus.
NCBI_TaxID=1422;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=2835089; DOI=10.1021/bi00404a033;
Tanizawa K., Ohshima A., Scheidegger A., Inagaki K., Tanaka H.,
Soda K.;
"Thermostable alanine racemase from Bacillus stearothermophilus: DNA
and protein sequence determination and secondary structure
prediction.";
Biochemistry 27:1311-1316(1988).
[2]
PROTEIN SEQUENCE OF 31-43.
PubMed=2496744; DOI=10.1021/bi00428a004;
Faraci W.S., Walsh C.T.;
"Mechanism of inactivation of alanine racemase by beta, beta, beta-
trifluoroalanine.";
Biochemistry 28:431-437(1989).
[3]
PROTEIN SEQUENCE OF 36-43.
PubMed=3730360; DOI=10.1021/bi00359a029;
Badet B., Inagaki K., Soda K., Walsh C.T.;
"Time-dependent inhibition of Bacillus stearothermophilus alanine
racemase by (1-aminoethyl)phosphonate isomers by isomerization to
noncovalent slowly dissociating enzyme-(1-aminoethyl)phosphonate
complexes.";
Biochemistry 25:3275-3282(1986).
[4]
MUTAGENESIS OF ARG-219.
PubMed=10194319; DOI=10.1021/bi982924t;
Sun S., Toney M.D.;
"Evidence for a two-base mechanism involving tyrosine-265 from
arginine-219 mutants of alanine racemase.";
Biochemistry 38:4058-4065(1999).
[5]
FUNCTION, ACTIVE SITES, AND MUTAGENESIS.
PubMed=10502689; DOI=10.1093/oxfordjournals.jbchem.a022517;
Watanabe A., Yoshimura T., Mikami B., Esaki N.;
"Tyrosine 265 of alanine racemase serves as a base abstracting alpha-
hydrogen from L-alanine: the counterpart residue to lysine 39 specific
to D-alanine.";
J. Biochem. 126:781-786(1999).
[6]
FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF TYR-354.
PubMed=12203980;
DOI=10.1002/1439-7633(20020802)3:8<789::AID-CBIC789>3.0.CO;2-D;
Patrick W.M., Weisner J., Blackburn J.M.;
"Site-directed mutagenesis of Tyr354 in Geobacillus stearothermophilus
alanine racemase identifies a role in controlling substrate
specificity and a possible role in the evolution of antibiotic
resistance.";
ChemBioChem 3:789-792(2002).
[7]
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL
PHOSPHATE, COFACTOR, SUBUNIT, PYRIDOXAL PHOSPHATE AT LYS-39, AND
SEQUENCE REVISION.
PubMed=9063881; DOI=10.1021/bi961856c;
Shaw J.P., Petsko G.A., Ringe D.;
"Determination of the structure of alanine racemase from Bacillus
stearothermophilus at 1.9-A resolution.";
Biochemistry 36:1329-1342(1997).
[8]
X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL
PHOSPHATE AND L-ALA PHOSPHONATE, COFACTOR, AND ACTIVE SITE.
PubMed=9671513; DOI=10.1021/bi980692s;
Stamper C.G., Morollo A.A., Ringe D.;
"Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a
stable external aldimine.";
Biochemistry 37:10438-10445(1998).
[9]
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS)IN COMPLEX WITH PYRIDOXAL
PHOSPHATE AND PROPIONATE, CATALYTIC ACTIVITY, SUBUNIT, COFACTOR,
PYRIDOXAL PHOSPHATE AT LYS-39, ENZYME REGULATION, AND CARBAMYLATION AT
LYS-129.
STRAIN=ATCC 12980 / DSM 22 / JCM 2501 / NBRC 12550 / NCIMB 8923 / NCTC
10339 / VKM B-510;
PubMed=10079072; DOI=10.1021/bi9822729;
Morollo A.A., Petsko G.A., Ringe D.;
"Structure of a Michaelis complex analogue: propionate binds in the
substrate carboxylate site of alanine racemase.";
Biochemistry 38:3293-3301(1999).
[10]
X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH D-ALANINE
PHOSPHONATE, AND CARBAMYLATION AT LYS-129.
Stamper G.F., Ringe D.;
"Crystal structure of alanine racemase in complex with D-alanine
phosphonate.";
Submitted (SEP-2000) to the PDB data bank.
[11]
X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEXES WITH
N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE AND
N-(5'-PHOSPHOPYRIDOXYL)-L-ALANINE, COFACTOR, ACTIVE SITE, PYRIDOXAL
PHOSPHATE AT LYS-39, AND CARBAMYLATION AT LYS-129.
PubMed=11886871; DOI=10.1074/jbc.M201615200;
Watanabe A., Yoshimura T., Mikami B., Hayashi H., Kagamiyama H.,
Esaki N.;
"Reaction mechanism of alanine racemase from Bacillus
stearothermophilus: x-ray crystallographic studies of the enzyme bound
with N-(5'-phosphopyridoxyl)alanine.";
J. Biol. Chem. 277:19166-19172(2002).
[12]
X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEXES WITH PYRIDOXAL
PHOSPHATE AND CYCLOSERINE, CATALYTIC ACTIVITY, ENZYME REGULATION,
COFACTOR, ACTIVE SITE, AND CARBAMYLATION AT LYS-129.
PubMed=12741835; DOI=10.1021/bi027022d;
Fenn T.D., Stamper G.F., Morollo A.A., Ringe D.;
"A side reaction of alanine racemase: transamination of cycloserine.";
Biochemistry 42:5775-5783(2003).
[13]
X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH CYCLOSERINE AND
PYRIDOXAL PHOSPHATE, COFACTOR, SUBUNIT, PYRIDOXAL PHOSPHATE AT LYS-39,
MUTAGENESIS OF TYR-265, ENZYME REGULATION, ACTIVE SITE, AND
CARBAMYLATION AT LYS-129.
PubMed=15807525; DOI=10.1021/bi047842l;
Fenn T.D., Holyoak T., Stamper G.F., Ringe D.;
"Effect of a Y265F mutant on the transamination-based cycloserine
inactivation of alanine racemase.";
Biochemistry 44:5317-5327(2005).
-!- FUNCTION: Catalyzes the interconversion of L-alanine and D-
alanine. Also weakly active on serine.
{ECO:0000269|PubMed:10502689, ECO:0000269|PubMed:12203980}.
-!- CATALYTIC ACTIVITY: L-alanine = D-alanine. {ECO:0000255|HAMAP-
Rule:MF_01201, ECO:0000269|PubMed:10079072,
ECO:0000269|PubMed:12203980, ECO:0000269|PubMed:12741835}.
-!- COFACTOR:
Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
Evidence={ECO:0000255|HAMAP-Rule:MF_01201,
ECO:0000269|PubMed:10079072, ECO:0000269|PubMed:11886871,
ECO:0000269|PubMed:12741835, ECO:0000269|PubMed:15807525,
ECO:0000269|PubMed:9063881, ECO:0000269|PubMed:9671513};
-!- ENZYME REGULATION: Inhibited by acetate and propionate.
Irreversibly inhibited by cycloserine.
{ECO:0000269|PubMed:10079072, ECO:0000269|PubMed:12741835,
ECO:0000269|PubMed:15807525}.
-!- PATHWAY: Amino-acid biosynthesis; D-alanine biosynthesis; D-
alanine from L-alanine: step 1/1. {ECO:0000255|HAMAP-
Rule:MF_01201}.
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10079072,
ECO:0000269|PubMed:15807525, ECO:0000269|PubMed:9063881,
ECO:0000269|PubMed:9671513, ECO:0000269|Ref.10}.
-!- SIMILARITY: Belongs to the alanine racemase family.
{ECO:0000255|HAMAP-Rule:MF_01201}.
-----------------------------------------------------------------------
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EMBL; M19142; AAA22220.1; -; Genomic_DNA.
PIR; A29984; A29984.
PDB; 1BD0; X-ray; 1.60 A; A/B=1-388.
PDB; 1EPV; X-ray; 2.20 A; A/B=2-388.
PDB; 1FTX; X-ray; 2.20 A; A/B=2-388.
PDB; 1L6F; X-ray; 2.00 A; A/B=1-388.
PDB; 1L6G; X-ray; 2.00 A; A/B=1-388.
PDB; 1NIU; X-ray; 2.20 A; A/B=1-388.
PDB; 1SFT; X-ray; 1.90 A; A/B=1-388.
PDB; 1XQK; X-ray; 1.95 A; A/B=1-382.
PDB; 1XQL; X-ray; 1.80 A; A/B=1-382.
PDB; 2SFP; X-ray; 1.90 A; A/B=1-388.
PDB; 3UW6; X-ray; 2.30 A; A/B/C=1-388.
PDB; 4ILS; X-ray; 2.50 A; A/B/C=1-388.
PDBsum; 1BD0; -.
PDBsum; 1EPV; -.
PDBsum; 1FTX; -.
PDBsum; 1L6F; -.
PDBsum; 1L6G; -.
PDBsum; 1NIU; -.
PDBsum; 1SFT; -.
PDBsum; 1XQK; -.
PDBsum; 1XQL; -.
PDBsum; 2SFP; -.
PDBsum; 3UW6; -.
PDBsum; 4ILS; -.
ProteinModelPortal; P10724; -.
SMR; P10724; -.
ChEMBL; CHEMBL1075086; -.
DrugBank; DB03801; Lysine Nz-Carboxylic Acid.
DrugBank; DB01993; N-(5'-Phosphopyridoxyl)-D-Alanine.
DrugBank; DB03766; Propanoic Acid.
DrugBank; DB02142; Pyridoxamine-5'-Phosphate.
DrugBank; DB04467; Pyridoxyl-Alanine-5-Phosphate.
DrugBank; DB03327; {1-[(3-Hydroxy-Methyl-5-Phosphonooxy-Methyl-Pyridin-4-Ylmethyl)-Amino]-Ethyl}-Phosphonic Acid.
BRENDA; 5.1.1.1; 623.
SABIO-RK; P10724; -.
UniPathway; UPA00042; UER00497.
EvolutionaryTrace; P10724; -.
GO; GO:0008784; F:alanine racemase activity; IEA:UniProtKB-EC.
GO; GO:0030632; P:D-alanine biosynthetic process; IEA:UniProtKB-UniPathway.
Gene3D; 2.40.37.10; -; 1.
Gene3D; 3.20.20.10; -; 1.
HAMAP; MF_01201; Ala_racemase; 1.
InterPro; IPR000821; Ala_racemase.
InterPro; IPR009006; Ala_racemase/Decarboxylase_C.
InterPro; IPR011079; Ala_racemase_C.
InterPro; IPR001608; Ala_racemase_N.
InterPro; IPR020622; Ala_racemase_pyridoxalP-BS.
InterPro; IPR029066; PLP-binding_barrel.
Pfam; PF00842; Ala_racemase_C; 1.
Pfam; PF01168; Ala_racemase_N; 1.
PRINTS; PR00992; ALARACEMASE.
SMART; SM01005; Ala_racemase_C; 1.
SUPFAM; SSF50621; SSF50621; 1.
SUPFAM; SSF51419; SSF51419; 1.
TIGRFAMs; TIGR00492; alr; 1.
PROSITE; PS00395; ALANINE_RACEMASE; 1.
1: Evidence at protein level;
3D-structure; Direct protein sequencing; Isomerase;
Pyridoxal phosphate.
CHAIN 1 388 Alanine racemase.
/FTId=PRO_0000114499.
ACT_SITE 39 39 Proton acceptor; specific for D-alanine.
{ECO:0000305|PubMed:10502689,
ECO:0000305|PubMed:15807525}.
ACT_SITE 265 265 Proton acceptor; specific for L-alanine.
{ECO:0000305|PubMed:10502689,
ECO:0000305|PubMed:15807525}.
BINDING 136 136 Substrate. {ECO:0000269|PubMed:11886871}.
BINDING 312 312 Substrate; via amide nitrogen.
{ECO:0000269|PubMed:11886871}.
MOD_RES 39 39 N6-(pyridoxal phosphate)lysine.
{ECO:0000269|PubMed:11886871,
ECO:0000269|PubMed:15807525,
ECO:0000269|PubMed:9063881}.
MOD_RES 129 129 N6-carboxylysine.
{ECO:0000269|PubMed:10079072,
ECO:0000269|PubMed:11886871,
ECO:0000269|PubMed:12741835,
ECO:0000269|PubMed:15807525,
ECO:0000269|Ref.10}.
MUTAGEN 39 39 K->A: Loss of activity.
{ECO:0000269|PubMed:10502689}.
MUTAGEN 166 166 H->A: 6.5-fold decrease in activity.
{ECO:0000269|PubMed:10502689}.
MUTAGEN 219 219 R->A: 100-fold decrease in activity.
{ECO:0000269|PubMed:10194319}.
MUTAGEN 219 219 R->E: 1000-fold decrease in activity.
{ECO:0000269|PubMed:10194319}.
MUTAGEN 219 219 R->K: 4-fold decrease in activity.
{ECO:0000269|PubMed:10194319}.
MUTAGEN 265 265 Y->A: 5000-fold decrease in activity.
{ECO:0000269|PubMed:15807525}.
MUTAGEN 265 265 Y->F: Loss of activity.
{ECO:0000269|PubMed:15807525}.
MUTAGEN 265 265 Y->S: 2000-fold decrease in activity.
{ECO:0000269|PubMed:15807525}.
MUTAGEN 354 354 Y->A: 54-fold increase in serine racemase
activity. {ECO:0000269|PubMed:12203980}.
MUTAGEN 354 354 Y->N: 81-fold increase in serine racemase
activity. {ECO:0000269|PubMed:12203980}.
MUTAGEN 354 354 Y->Q: 51-fold increase in serine racemase
activity. {ECO:0000269|PubMed:12203980}.
CONFLICT 37 38 VV -> PP (in Ref. 3; AA sequence).
{ECO:0000305}.
CONFLICT 57 62 AGASRL -> RGPPP (in Ref. 1; AAA22220).
{ECO:0000305}.
CONFLICT 288 289 WL -> V (in Ref. 1; AAA22220).
{ECO:0000305}.
STRAND 6 13 {ECO:0000244|PDB:1BD0}.
HELIX 14 27 {ECO:0000244|PDB:1BD0}.
STRAND 33 37 {ECO:0000244|PDB:1BD0}.
HELIX 39 43 {ECO:0000244|PDB:1BD0}.
HELIX 47 57 {ECO:0000244|PDB:1BD0}.
STRAND 61 66 {ECO:0000244|PDB:1BD0}.
HELIX 67 75 {ECO:0000244|PDB:1BD0}.
STRAND 82 84 {ECO:0000244|PDB:1BD0}.
HELIX 90 92 {ECO:0000244|PDB:1BD0}.
HELIX 93 98 {ECO:0000244|PDB:1BD0}.
STRAND 101 105 {ECO:0000244|PDB:1BD0}.
HELIX 108 117 {ECO:0000244|PDB:1BD0}.
STRAND 124 130 {ECO:0000244|PDB:1BD0}.
STRAND 132 134 {ECO:0000244|PDB:1BD0}.
STRAND 136 139 {ECO:0000244|PDB:1BD0}.
HELIX 142 154 {ECO:0000244|PDB:1BD0}.
STRAND 158 164 {ECO:0000244|PDB:1BD0}.
STRAND 172 174 {ECO:0000244|PDB:1XQK}.
HELIX 176 189 {ECO:0000244|PDB:1BD0}.
STRAND 192 194 {ECO:0000244|PDB:1SFT}.
STRAND 197 200 {ECO:0000244|PDB:1BD0}.
HELIX 204 209 {ECO:0000244|PDB:1BD0}.
HELIX 211 213 {ECO:0000244|PDB:1XQL}.
STRAND 217 220 {ECO:0000244|PDB:1BD0}.
HELIX 222 225 {ECO:0000244|PDB:1BD0}.
HELIX 231 236 {ECO:0000244|PDB:1BD0}.
STRAND 245 250 {ECO:0000244|PDB:1BD0}.
STRAND 252 257 {ECO:0000244|PDB:1BD0}.
STRAND 262 264 {ECO:0000244|PDB:1BD0}.
HELIX 265 267 {ECO:0000244|PDB:1BD0}.
STRAND 273 281 {ECO:0000244|PDB:1BD0}.
HELIX 284 286 {ECO:0000244|PDB:1BD0}.
HELIX 290 294 {ECO:0000244|PDB:1BD0}.
STRAND 296 299 {ECO:0000244|PDB:1BD0}.
STRAND 302 308 {ECO:0000244|PDB:1BD0}.
STRAND 315 318 {ECO:0000244|PDB:1BD0}.
STRAND 328 335 {ECO:0000244|PDB:1BD0}.
STRAND 338 340 {ECO:0000244|PDB:1BD0}.
HELIX 342 349 {ECO:0000244|PDB:1BD0}.
HELIX 355 359 {ECO:0000244|PDB:1BD0}.
STRAND 366 370 {ECO:0000244|PDB:1BD0}.
STRAND 373 378 {ECO:0000244|PDB:1BD0}.
SEQUENCE 388 AA; 43593 MW; F54AA581F135EA7A CRC64;
MNDFHRDTWA EVDLDAIYDN VENLRRLLPD DTHIMAVVKA NAYGHGDVQV ARTALEAGAS
RLAVAFLDEA LALREKGIEA PILVLGASRP ADAALAAQQR IALTVFRSDW LEEASALYSG
PFPIHFHLKM DTGMGRLGVK DEEETKRIVA LIERHPHFVL EGLYTHFATA DEVNTDYFSY
QYTRFLHMLE WLPSRPPLVH CANSAASLRF PDRTFNMVRF GIAMYGLAPS PGIKPLLPYP
LKEAFSLHSR LVHVKKLQPG EKVSYGATYT AQTEEWIGTI PIGYADGWLR RLQHFHVLVD
GQKAPIVGRI CMDQCMIRLP GPLPVGTKVT LIGRQGDEVI SIDDVARHLE TINYEVPCTI
SYRVPRIFFR HKRIMEVRNA IGRGESSA


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